Prognostic characteristics of a six-gene signature based on ssGSEA in sarcoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38240704", "kind": "science-record", "revision": 3, "content_hash": "sha256:eba57a741bbf5ba735519119ccff761d0c80683d31b46b453c12ff2c7498d127", "created_at": "2026-11-01T19:20:09Z", "updated_at": "2026-11-01T22:11:03Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Prognostic characteristics of a six-gene signature based on ssGSEA in sarcoma.", "doi": "10.18632/aging.205443", "pmid": "38240704", "authors": ["Jun Liu", "Jianjun Lu", "Gefei Wang", "Liming Gu", "Wenli Li"], "journal": "Aging", "year": 2024, "abstract": "BACKGROUND: Sarcoma is a rare malignant tumor originating of the interstitial or connective tissue with a poor prognosis. Next-generation sequencing technology offers new opportunities for accurate diagnosis and treatment of sarcomas. There is an urgent need for new gene signature to predict prognosis and evaluate treatment outcomes.\nMETHODS: We used transcriptome data from the Cancer Genome Atlas (TCGA) database and single sample gene set enrichment analysis (ssGSEA) to explore the cancer hallmarks most associated with prognosis in sarcoma patients. Then, weighted gene coexpression network analysis, univariate COX regression analysis and random forest algorithm were used to construct prognostic gene characteristics. Finally, the prognostic value of gene markers was validated in the TCGA and Integrated Gene Expression (GEO) (GSE17118) datasets, respectively.\nRESULTS: MYC targets V1 and V2 are the main cancer hallmarks affecting the overall survival (OS) of sarcoma patients. A six-gene signature including VEGFA, HMGB3, FASN, RCC1, NETO2 and BIRC5 were constructed. Kaplan-Meier analysis suggested that higher risk scores based on the six-gene signature associated with poorer OS (P < 0.001). The receiver Operating characteristic curve showed that the risk score based on the six-gene signature was a good predictor of sarcoma, with an area under the curve (AUC) greater than 0.73. In addition, the prognostic value of the six-gene signature was validated in GSE17118 with an AUC greater than 0.72.\nCONCLUSION: This six-gene signature is an independent prognostic factor in patients with sarcoma and is expected to be a potential therapeutic target for sarcoma.", "claims": [{"id": "claim-method", "statement": "Each parameter’s importance to overall survival was assessed with a Cox proportional hazards regression model.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38240704", "locator": "sections[5] \"Survival analysis based on risk scores\" paragraph 2", "quote": "Each parameter’s importance to overall survival was assessed with a Cox proportional hazards regression model."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets analyzed in the current study are available in the TCGA repository (http://cancergenome.nih.gov/) and the GEO (https://www.ncbi.nlm.nih.gov/geo/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38240704", "locator": "sections[12] \"Availability of data and materials\" paragraph 2", "quote": "The datasets analyzed in the current study are available in the TCGA repository (http://cancergenome.nih.gov/) and the GEO (https://www.ncbi.nlm.nih.gov/geo/)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "In the TCGA-SARC cohort, higher MYC targets V1 and V2 Z-scores were associated with poorer overall survival.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38240704", "locator": "sections[15] \"MYC targets V1 and V2 were identified as critical survival factors in sarcoma\" paragraph 2", "quote": "In the high MYC targets V1 Z-score group, overall survival rates were lower than that in the low MYC targets V1 Z-score group (HR = 1.90, P = 0.002; Figure 2C)."}, {"asset": "source:pmid:38240704", "locator": "sections[15] \"MYC targets V1 and V2 were identified as critical survival factors in sarcoma\" paragraph 2", "quote": "Similarly, in the high MYC targets V2 Z-score group, overall survival rates were lower than that in the low MYC targets V2 Z-score group (HR = 1.61, P = 0.019; Figure 2E)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "In the TCGA-SARC cohort, higher MYC targets V1 and V2 Z-scores were associated with poorer overall survival.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:38240704"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE17118"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE17118"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38240704", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.18632/aging.205443", "sha256": "sha256:a3dc01f93f4e67a6d190a454455e5e743ea8b3f315e2420671eea44b13bc31cd", "bytes": 40845, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.18632/aging.205443", "version": null, "note": "Full article fetched from PMC; 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